Benefits and Challenges of Pre-clustered Network-Based Pathway Analysis.

ABSTRACT: Functional analysis of gene sets derived from experiments is typically done by pathway annotation. Although many algorithms exist for analyzing the association between a gene set and a pathway, an issue which is generally ignored is that gene sets often represent multiple pathways. In such cases an association to a pathway is weakened by the presence of genes associated with other pathways. A way to counteract this is to cluster the gene set into more homogenous parts before performing pathway analysis on each module. We explored whether network-based pre-clustering of a query gene set can improve pathway analysis. The methods MCL, Infomap, and MGclus were used to cluster the gene set projected onto the FunCoup network. We characterized how well these methods are able to detect individual

SUBMITTER: Castresana-Aguirre M 

PROVIDER: S-EPMC9127507 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature